Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate AZOBR_RS18890 AZOBR_RS18890 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__azobra:AZOBR_RS18890 Length = 411 Score = 298 bits (762), Expect = 5e-85 Identities = 160/406 (39%), Positives = 261/406 (64%), Gaps = 9/406 (2%) Query: 341 VVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENPDP 400 +V+KFGG ++ D+++++ VA K+ + K+G + VV+SAM T+ L++ ID+ D Sbjct: 4 IVLKFGGTSVGDIDRIKNVARKVEQEVKAGHQVAVVVSAMSGVTNQLVKYCNDIDKLHDA 63 Query: 401 RELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDIISR 460 RE D ++++GE + L++IAL+ G +A S+ G Q+ I +D+ +G ARI+ I+T + + Sbjct: 64 REYDAIVASGEQVTSGLLAIALQSLGIQARSWLGWQIPIYSDETHGKARIVSIDTAELDK 123 Query: 461 YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVDGVYTADP 520 + + VVAGFQG+TETG ITTLGRGGSD +A+ALA +L AD C++Y DVDGVYT DP Sbjct: 124 RMNTGEVAVVAGFQGVTETGRITTLGRGGSDTSAVALAAALKADRCDIYTDVDGVYTTDP 183 Query: 521 RIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETRGT----- 575 RIV AR + ++++EEM+EL+ GA+VLQ R+ E A + V+V + ++ +E G+ Sbjct: 184 RIVTKARKLSKITYEEMLELASQGAKVLQTRSVEMAMNHRVRVQVLSSFEEAAGSALPGT 243 Query: 576 -LIWEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGM- 633 ++ E VE +V + + AK+ L V D+PGVAA I L+ VN+DMI+Q + Sbjct: 244 LVVDEDEIVEKEVVSGIAYSRDEAKITLIGVADRPGVAASIFGPLTDAAVNVDMIVQNVS 303 Query: 634 KSGEYNTVAFIVPESQLGKLDIDLLKTRSEA--KEIIIEKGLAKVSIVGVNLTSTPEISA 691 + G+ + F V ++ + + L ++E K I+ + + KVS++GV + S ++ Sbjct: 304 EDGKSTDMTFTVGKADIARAVKVLEDAQAELNYKRIVSDANVVKVSVIGVGMRSHAGVAQ 363 Query: 692 TLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 +F+ LA++GINI +IS S +ISV+I +Y E A++A+H+ + LD Sbjct: 364 RMFKALADKGINIQVISTSEIKISVLIAEEYAELALRALHTAYGLD 409 Lambda K H 0.318 0.137 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 638 Number of extensions: 29 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 411 Length adjustment: 36 Effective length of query: 703 Effective length of database: 375 Effective search space: 263625 Effective search space used: 263625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory